State logging in chemical reaction networks

Abstract

Recording the state of a molecular programmed nanosystem is essential for many purposes. The capability to log the state helps in debugging and verifying the system, enables checkpointing for rollback in case of faults, and provides stable system states for input into other devices. In this paper we present the computational design of a molecular device to log the states of a system modeled by a chemical reaction network. We describe, formally specify and prove the correctness of the design. We then extend the device to include components that detect whether a signal is valid and log only valid states. These molecular components enable us to store a copy of the system's state and to communicate that copy to another system for use.